2ORG

Directing Macromolecular Conformation Through Halogen Bonds


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Directing macromolecular conformation through halogen bonds.

Voth, A.R.Hays, F.A.Ho, P.S.

(2007) Proc Natl Acad Sci U S A 104: 6188-6193

  • DOI: https://doi.org/10.1073/pnas.0610531104
  • Primary Citation of Related Structures:  
    2ORF, 2ORG, 2ORH

  • PubMed Abstract: 

    The halogen bond, a noncovalent interaction involving polarizable chlorine, bromine, or iodine molecular substituents, is now being exploited to control the assembly of small molecules in the design of supramolecular complexes and new materials. We demonstrate that a halogen bond formed between a brominated uracil and phosphate oxygen can be engineered to direct the conformation of a biological molecule, in this case to define the conformational isomer of a four-stranded DNA junction when placed in direct competition against a classic hydrogen bond. As a result, this bromine interaction is estimated to be approximately 2-5 kcal/mol stronger than the analogous hydrogen bond in this environment, depending on the geometry of the halogen bond. This study helps to establish halogen bonding as a potential tool for the rational design and construction of molecular materials with DNA and other biological macromolecules.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331-7503, USA.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*GP*GP*TP*AP*(BRU)P*CP*GP*G)-3')10N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*CP*GP*AP*TP*AP*CP*CP*GP*G)-3')10N/A
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.218 
  • R-Value Observed: 0.218 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.779α = 90
b = 24.403β = 111.07
c = 37.316γ = 90
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
EPMRphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2007-03-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description